Genetic Variant WDR27:c.2524-9_2524-4delTTTTTT (chr6-169572543-CAAAAAA-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_182552.5(WDR27):c.2524-9_2524-4delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.030 ( 40 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

WDR27
NM_182552.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Variant links:

Genes affected

WDR27 (HGNC:21248): (WD repeat domain 27) This gene encodes a protein with multiple WD repeats. Proteins with these repeats may form scaffolds for protein-protein interaction and play key roles in cell signalling. Alternative splicing results in multiple transcript variants, but the full-length structure of some of these variants cannot be determined. [provided by RefSeq, Nov 2015]

WDR27 links:

ENSG00000285733 (HGNC:):

ENSG00000285733 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 6-169572543-CAAAAAA-C is Benign according to our data. Variant chr6-169572543-CAAAAAA-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR27	NM_182552.5 link	c.2524-9_2524-4delTTTTTT		splice_region_variant, intron_variant	Intron 24 of 25	ENST00000448612.6	NP_872358.4	A2RRH5-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6 link	c.2524-9_2524-4delTTTTTT		splice_region_variant, intron_variant	Intron 24 of 25	1	NM_182552.5	ENSP00000416289.1		A2RRH5-4
ENSG00000285733	ENST00000648086.1 link	c.533+10287_533+10292delTTTTTT		intron_variant	Intron 5 of 7			ENSP00000497979.1		A0A3B3ITY5

Frequencies

GnomAD3 genomes

AF:

0.0304

AC:

2809

AN:

92286

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0296

Gnomad AMI

AF:

0.00424

Gnomad AMR

AF:

0.0212

Gnomad ASJ

AF:

0.0573

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.0590

Gnomad FIN

AF:

0.0414

Gnomad MID

AF:

0.0347

Gnomad NFE

AF:

0.0241

Gnomad OTH

AF:

0.0291

GnomAD3 exomes

AF:

0.100

AC:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

Gnomad NFE exome

AF:

0.100

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.0305

AC:

2814

AN:

92268

Hom.:

Cov.:

AF XY:

0.0329

AC XY:

1405

AN XY:

42690

show subpopulations

Gnomad4 AFR

AF:

0.0296

Gnomad4 AMR

AF:

0.0212

Gnomad4 ASJ

AF:

0.0573

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.0596

Gnomad4 FIN

AF:

0.0414

Gnomad4 NFE

AF:

0.0241

Gnomad4 OTH

AF:

0.0321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over